2023
Authors
Patrício, C; Teixeira, LF; Neves, JC;
Publication
CoRR
Abstract
2024
Authors
Miranda, I; Agrotis, G; Tan, RB; Teixeira, LF; Silva, W;
Publication
46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2024, Orlando, FL, USA, July 15-19, 2024
Abstract
Breast cancer, the most prevalent cancer among women, poses a significant healthcare challenge, demanding effective early detection for optimal treatment outcomes. Mammography, the gold standard for breast cancer detection, employs low-dose X-rays to reveal tissue details, particularly cancerous masses and calcium deposits. This work focuses on evaluating the impact of incorporating anatomical knowledge to improve the performance and robustness of a breast cancer classification model. In order to achieve this, a methodology was devised to generate anatomical pseudo-labels, simulating plausible anatomical variations in cancer masses. These variations, encompassing changes in mass size and intensity, closely reflect concepts from the BI-RADs scale. Besides anatomical-based augmentation, we propose a novel loss term promoting the learning of cancer grading by our model. Experiments were conducted on publicly available datasets simulating both in-distribution and out-of-distribution scenarios to thoroughly assess the model's performance under various conditions.
2025
Authors
Patrício, C; Torto, IR; Cardoso, JS; Teixeira, LF; Neves, J;
Publication
Comput. Biol. Medicine
Abstract
The main challenges limiting the adoption of deep learning-based solutions in medical workflows are the availability of annotated data and the lack of interpretability of such systems. Concept Bottleneck Models (CBMs) tackle the latter by constraining the model output on a set of predefined and human-interpretable concepts. However, the increased interpretability achieved through these concept-based explanations implies a higher annotation burden. Moreover, if a new concept needs to be added, the whole system needs to be retrained. Inspired by the remarkable performance shown by Large Vision-Language Models (LVLMs) in few-shot settings, we propose a simple, yet effective, methodology, CBVLM, which tackles both of the aforementioned challenges. First, for each concept, we prompt the LVLM to answer if the concept is present in the input image. Then, we ask the LVLM to classify the image based on the previous concept predictions. Moreover, in both stages, we incorporate a retrieval module responsible for selecting the best examples for in-context learning. By grounding the final diagnosis on the predicted concepts, we ensure explainability, and by leveraging the few-shot capabilities of LVLMs, we drastically lower the annotation cost. We validate our approach with extensive experiments across four medical datasets and twelve LVLMs (both generic and medical) and show that CBVLM consistently outperforms CBMs and task-specific supervised methods without requiring any training and using just a few annotated examples. More information on our project page: https://cristianopatricio.github.io/CBVLM/. © 2025 Elsevier B.V., All rights reserved.
2024
Authors
Rio-Torto, I; Cardoso, JS; Teixeira, LF;
Publication
MEDICAL IMAGING WITH DEEP LEARNING
Abstract
The increased interest and importance of explaining neural networks' predictions, especially in the medical community, associated with the known unreliability of saliency maps, the most common explainability method, has sparked research into other types of explanations. Natural Language Explanations (NLEs) emerge as an alternative, with the advantage of being inherently understandable by humans and the standard way that radiologists explain their diagnoses. We extend upon previous work on NLE generation for multi-label chest X-ray diagnosis by replacing the traditional decoder-only NLE generator with an encoder-decoder architecture. This constitutes a first step towards Reinforcement Learning-free adversarial generation of NLEs when no (or few) ground-truth NLEs are available for training, since the generation is done in the continuous encoder latent space, instead of in the discrete decoder output space. However, in the current scenario, large amounts of annotated examples are still required, which are especially costly to obtain in the medical domain, given that they need to be provided by clinicians. Thus, we explore how the recent developments in Parameter-Efficient Fine-Tuning (PEFT) can be leveraged for this usecase. We compare different PEFT methods and find that integrating the visual information into the NLE generator layers instead of only at the input achieves the best results, even outperforming the fully fine-tuned encoder-decoder-based model, while only training 12% of the model parameters. Additionally, we empirically demonstrate the viability of supervising the NLE generation process on the encoder latent space, thus laying the foundation for RL-free adversarial training in low ground-truth NLE availability regimes. The code is publicly available at https://github.com/icrto/peft-nles.
2025
Authors
Aubard, M; Madureira, A; Teixeira, L; Pinto, J;
Publication
IEEE JOURNAL OF OCEANIC ENGINEERING
Abstract
With the growing interest in underwater exploration and monitoring, autonomous underwater vehicles have become essential. The recent interest in onboard deep learning (DL) has advanced real-time environmental interaction capabilities relying on efficient and accurate vision-based DL models. However, the predominant use of sonar in underwater environments, characterized by limited training data and inherent noise, poses challenges to model robustness. This autonomy improvement raises safety concerns for deploying such models during underwater operations, potentially leading to hazardous situations. This article aims to provide the first comprehensive overview of sonar-based DL under the scope of robustness. It studies sonar-based DL perception task models, such as classification, object detection, segmentation, and simultaneous localization and mapping. Furthermore, this article systematizes sonar-based state-of-the-art data sets, simulators, and robustness methods, such as neural network verification, out-of-distribution, and adversarial attacks. This article highlights the lack of robustness in sonar-based DL research and suggests future research pathways, notably establishing a baseline sonar-based data set and bridging the simulation-to-reality gap.
2024
Authors
Aubard, M; Antal, L; Madureira, A; Teixeira, LF; Ábrahám, E;
Publication
CoRR
Abstract
This paper introduces ROSAR, a novel framework enhancing the robustness of deep learning object detection models tailored for side-scan sonar (SSS) images, generated by autonomous underwater vehicles using sonar sensors. By extending our prior work on knowledge distillation (KD), this framework integrates KD with adversarial retraining to address the dual challenges of model efficiency and robustness against SSS noises. We introduce three novel, publicly available SSS datasets, capturing different sonar setups and noise conditions. We propose and formalize two SSS safety properties and utilize them to generate adversarial datasets for retraining. Through a comparative analysis of projected gradient descent (PGD) and patch-based adversarial attacks, ROSAR demonstrates significant improvements in model robustness and detection accuracy under SSS-specific conditions, enhancing the model's robustness by up to 1.85%. ROSAR is available at https://github.com/remaro-network/ROSAR-framework.
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